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Sample GSM285284 Query DataSets for GSM285284
Status Public on Apr 30, 2008
Title E_071203_02_DS8382_W A
Sample type genomic
 
Source name HL-60;ATCC:CCL-240;promyeloblast;leukemia;blood;adult/female;DMEM;HL60;DnaseI enriched
Organism Homo sapiens
Characteristics HL60; ATCC
Treatment protocol Cells were lysed and Intact nuclei were isolated using NP40 and treated for 3 minutes with varying concentrations of DNaseI
Growth protocol (follow vendor recommendations for medium) with 2 mM L-glutamine adjusted to contain 1.5 g-L sodium bicarbonate. 4.5 g-L glucose. 10 mM HEPES and 1.0 mM sodium pyruvate and supplemented with 0.5 mg-ml G418 and 10percent fetal bovine serum
Extracted molecule genomic DNA
Extraction protocol Samples were extracted with an equal volume of Phenol and Chloroform and small fragments separated out by running the sample through a 10% sucrose cushion for 24 hrs at 25000 rpm on a Beckman Ultracentrfuge using a SW41 rotor.
Label biotin
Label protocol Fragments were cleaned using Qiagen PCR columns. Samples were amplified using the Sigma WGA amplification kit. Cleaned and fragmented to an avg size of 75 bp using DNaseI and labeled with Biotin 16-ddUTP and Terminal Transferase. (See Affymetrix Chip Chip protocol)
 
Hybridization protocol Labeled samples were hybridized for 16 hr at 45C on Affymetrix whole Genome Tiling Arrays. Arrays were washed and post stained using the Affymetrix 450 Fluidics Station.
Scan protocol Arrays were scanned using an Affymetrix GeneChip Scanner 3000.
Description DnaseI enriched
Data processing Cel files were generated using Affymetrix's GCOS software and Analyzed using the Affymetrix TAS analysis software; linearly scaled to intesity of 500, 2-sided upper quantile normalization.
 
Submission date Apr 29, 2008
Last update date Apr 29, 2008
Contact name John A Stamatoyannopoulos
E-mail(s) jstam@altius.org
Organization name Altius Institute / University of Washington
Department Genome Sciences
Lab Stamatoyannopoulos
Street address 2211 Elliott Avenue, 4th Floor
City SEATTLE
State/province WA
ZIP/Postal code 98121
Country USA
 
Platform ID GPL4910
Series (1)
GSE11298 Tissue/Cell DNaseI sensitivity/hypersensitivity screening II

Supplementary file Size Download File type/resource
GSM285284.CEL.gz 26.9 Mb (ftp)(http) CEL
GSM285284.bed.gz 71.7 Mb (ftp)(http) BED
Processed data provided as supplementary file

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